Aperture Losing Connection With Masters

Hi,
I've been using iPhoto since the beginning and started noticing over the past year it would lose connections with the master files. Thankfully I had backups of each file. So I decided to start rebuilding my library in Aperture from scratch (figured start clean and all). I started importing files and adding metadata and keywords. I didn't get far (literally a day or two) before I realized that Aperture started losing conncetions with the Master files as well.
How I found out is that I used a software called HoudahGeo to geotag some old photos and it gave me the warning that it couldn't find the master files. When I went back to Aperture I clicked on the image and noticed that the "Show in Finder" option was grayed out. I went into the Aperture library itself (because I was having it keep on the images inside the library and not referenced) and noticed that the files were there in the "Masters" folder but Aperture was saying it was missing. When I tried to relocate the original it fixed the one image but then started to break connections with other files and images. I notice it had randomly last connection with different files in different albums.
At this point I'm not sure what to do since I've had this problem with both iPhoto and Aperture. Thankfully I didn't get far before I realized this problem but I was really hoping to use Aperture for all my photos but it makes me worried that it'll lose images like that. I don't want images to get deleted or lost.
Has anyone had this problem or know how to fix it? I sent feedback to Apple so hoping it's a bug they can fix. I'm currently using Mavericks and Aperture 3.5.1.
Thanks!

How I found out is that I used a software called HoudahGeo to geotag some old photos and it gave me the warning that it couldn't find the master files. When I went back to Aperture I clicked on the image and noticed that the "Show in Finder" option was grayed out.
I thought your Aperture library is managed? iPhoto will show the originals for managed images, but not Aperture. "Show in Finder" will be grayed out, if the images is in the Aperture Library package. That does not indicate that Aperture has lost the connection. Broken arrow badges indicate lost originals.
But the problem wasn't HoudahGeo accessing my masters but notifying me that Aperture lost them. Because when I went back to into Aperture I noticed the original files were missing.
What exacty did you see in Aperture, that the orignals are missing? Badges with broken arrows?
I went into the Aperture library itself (because I was having it keep on the images inside the library and not referenced) and noticed that the files were there in the "Masters" folder but Aperture was saying it was missing. When I tried to relocate the original it fixed the one image but then started to break connections with other files and images.
This cannot be - are you saying, Aperture did relocate an original file, that it reported as missing?
The forum software seems to be working again today, so we could start again to try to get to the roots of your puzzling problem.
Or have you solved it by now? Then let us know please.

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